genome.fa.s3.2.7.7.80.10.50.1000.12.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   

This is table  12  of  32  ( 3795 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1464769--1464918	82	1.9	82	81	6	191	55	2	2	40	1.25
1464769--1464949	78	2.2	82	77	8	190	55	2	1	40	1.24
1465414--1465461	11	4.5	11	77	15	55	31	2	0	66	1.03
1465453--1465487	17	2.0	18	94	5	63	57	0	0	42	0.99
1465586--1465631	23	2.0	22	95	4	83	41	13	0	45	1.43
1468421--1468456	2	18.0	2	94	0	63	47	0	0	52	1.00
1470618--1470686	13	5.8	12	77	17	56	52	2	0	44	1.16
1470930--1471020	6	15.3	6	72	15	64	36	0	0	63	0.94
1470978--1471035	13	4.4	14	77	16	52	39	0	0	60	0.97
1470933--1471020	19	5.1	18	72	21	64	36	0	0	63	0.95
1471208--1471288	24	3.5	23	71	8	74	41	0	0	58	0.98
1471202--1471288	46	1.9	45	86	6	122	43	0	0	56	0.99
1471587--1471611	2	12.5	2	100	0	50	0	52	0	48	1.00
1472464--1472499	3	12.0	3	100	0	72	66	0	33	0	0.92
1473446--1473667	111	2.0	111	91	1	365	22	36	18	22	1.94
1475295--1475347	26	2.0	26	100	0	106	37	15	22	24	1.92
1476310--1476358	15	3.4	14	80	8	53	18	2	4	75	1.06
1482571--1482607	2	19.0	2	94	5	67	51	0	0	48	1.00
1483361--1483437	28	2.6	32	76	14	83	57	0	0	42	0.99
1488190--1488292	50	2.0	54	86	9	151	49	0	2	46	1.23
1488637--1488695	27	2.1	27	78	3	73	44	0	1	54	1.10
1493214--1493249	2	18.5	2	88	5	56	47	2	0	50	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1495504--1495584	33	2.5	33	88	10	121	55	1	1	41	1.15
1495528--1495586	18	3.5	17	75	25	63	54	0	0	45	0.99
1495652--1495682	2	15.5	2	93	0	53	51	3	0	45	1.17
1495671--1495721	24	2.1	25	92	3	86	49	3	5	41	1.45
1499105--1499157	17	3.1	16	76	10	52	54	0	0	45	0.99
1499584--1499628	18	2.5	18	89	7	65	46	0	0	53	1.00
1499591--1499629	17	2.3	16	87	12	60	43	0	0	56	0.99
1499628--1499673	19	2.4	19	88	3	74	47	2	0	50	1.13
1500279--1500320	19	2.3	19	88	8	61	54	7	4	33	1.49
1500462--1500499	6	6.3	6	85	11	51	50	0	0	50	1.00
1500455--1500491	18	2.1	18	89	0	56	54	0	0	45	1.00
1500466--1500499	11	2.9	12	86	8	52	47	0	0	52	1.00
1500979--1501013	4	8.8	4	100	0	70	22	0	0	77	0.78
1515069--1515182	33	3.5	31	81	10	113	48	0	0	50	1.13
1515129--1515184	16	3.5	16	73	9	60	50	1	0	48	1.11
1515420--1515445	13	2.0	13	100	0	52	30	0	0	69	0.89
1521578--1521616	14	2.6	15	88	8	53	33	0	10	56	1.33
1524073--1524106	16	2.1	16	100	0	68	17	17	17	47	1.84
1525305--1525338	17	1.9	17	94	5	59	55	0	2	41	1.15
1525310--1525338	9	3.3	9	90	9	51	55	0	0	44	0.99
1529703--1529736	2	17.0	2	100	0	68	50	0	0	50	1.00
1531894--1531935	17	2.4	18	80	11	52	30	7	0	61	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1532648--1532761	17	6.5	17	72	22	69	56	0	0	42	1.05
1532625--1532756	49	3.0	43	74	21	112	57	0	0	41	1.04
1532642--1532761	16	6.8	18	70	19	85	56	0	0	42	1.05
1532619--1532758	16	8.9	16	68	18	64	58	0	0	40	1.03
1535777--1535823	2	23.5	2	100	0	94	51	0	0	48	1.00
1536035--1536070	2	18.0	2	100	0	72	50	0	0	50	1.00
1536068--1536125	27	2.1	27	93	0	98	55	0	10	34	1.34
1536068--1536138	27	2.6	27	88	0	97	52	0	12	35	1.40
1536994--1537023	5	5.8	5	92	7	51	20	0	0	80	0.72
1536994--1537023	11	2.8	11	95	5	53	20	0	0	80	0.72
1537909--1537939	16	2.0	16	93	6	55	58	0	0	41	0.98
1540624--1540657	17	2.0	17	100	0	68	64	0	23	11	1.26
1542859--1542994	67	2.0	67	100	0	272	32	17	19	30	1.95
1547554--1547599	15	3.1	15	75	12	51	28	0	0	71	0.86
1547554--1547607	20	2.5	22	76	17	58	29	1	0	68	1.00
1547558--1547601	20	2.2	20	87	4	61	29	0	0	70	0.88
1553793--1553929	62	2.2	62	88	3	206	52	2	0	44	1.18
1554594--1554682	45	2.0	45	83	12	114	49	0	1	49	1.08
1554778--1554844	20	3.4	19	73	20	57	64	2	1	31	1.18
1554979--1555030	22	2.3	22	80	3	59	48	7	0	44	1.31
1555751--1555806	21	2.6	22	75	13	55	44	1	3	50	1.29
1555921--1555964	18	2.4	19	85	14	65	40	0	0	59	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1555962--1555994	16	2.1	16	88	5	50	57	3	0	39	1.14
1555988--1556039	21	2.5	21	87	0	68	59	7	0	32	1.26
1555990--1556051	21	2.7	23	75	17	65	61	6	0	32	1.21
1556858--1556883	11	2.4	11	100	0	52	7	23	0	69	1.14
1558808--1558862	24	2.5	20	76	23	65	27	1	1	69	1.09
1562464--1562503	21	1.9	21	85	10	55	67	2	5	25	1.23
1562788--1562821	15	2.1	17	89	10	54	52	0	0	47	1.00
1563060--1563100	14	2.8	15	82	13	50	43	0	0	56	0.99
1564760--1564816	29	1.9	29	82	3	69	47	0	1	50	1.11
1565450--1565487	2	20.0	2	84	10	53	50	0	0	50	1.00
1566862--1566948	38	2.3	38	97	0	165	58	0	6	34	1.25
1566940--1566977	19	2.0	20	85	15	53	57	0	0	42	0.98
1571319--1571361	2	21.5	2	85	0	59	44	4	0	51	1.22
1571667--1571706	20	2.0	20	85	0	53	42	0	2	55	1.13
1572014--1572159	22	6.8	21	70	18	79	57	0	3	39	1.16
1572034--1572089	16	3.4	16	85	9	78	66	0	0	33	0.92
1572034--1572123	5	18.0	5	75	15	71	60	0	2	37	1.09
1572013--1572118	32	3.2	33	82	12	112	59	0	3	36	1.16
1572034--1572132	28	3.4	28	74	21	73	60	0	2	37	1.08
1572597--1572626	2	15.0	2	100	0	60	50	50	0	0	1.00
1572626--1572654	2	15.0	2	92	7	51	48	0	0	51	1.00
1584206--1584686	252	1.9	249	88	3	725	38	20	18	22	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1588050--1588094	17	2.8	16	80	12	56	60	0	0	40	0.97
1588160--1588208	17	2.8	17	75	3	53	44	0	0	55	0.99
1588133--1588193	17	3.8	17	68	18	58	37	1	0	60	1.07
1589291--1589385	29	3.2	31	87	10	130	47	10	9	32	1.70
1691126--1691217	32	2.9	32	91	3	152	30	8	8	52	1.62
1692302--1692369	16	4.1	16	67	22	50	52	0	0	47	1.00
1692306--1692385	31	2.5	34	84	11	100	57	0	0	42	0.98
1692318--1692385	34	2.1	33	86	8	95	55	0	0	44	0.99
1693911--1693949	19	2.1	19	85	0	51	53	0	0	46	1.00
1698030--1698084	25	2.2	25	83	6	67	36	1	3	58	1.26
1698613--1698648	3	12.0	3	100	0	72	33	0	0	66	0.92
1698816--1698913	12	7.9	13	69	21	59	56	1	1	41	1.13
1698882--1698923	19	2.3	18	84	12	50	59	0	0	40	0.97
1698893--1698973	37	2.2	36	81	12	94	44	0	0	55	0.99
1698891--1698955	17	3.6	18	74	23	57	50	0	0	49	1.00
1698881--1698962	9	9.2	9	70	20	57	50	0	0	50	1.00
1703230--1703256	2	13.5	2	100	0	54	51	48	0	0	1.00
1706361--1706390	15	2.0	15	93	0	51	33	6	10	50	1.62
1715769--1715805	19	2.0	19	89	5	58	70	0	0	29	0.88
1716623--1716668	20	2.3	20	88	0	65	54	2	0	43	1.12
1718358--1718415	19	2.8	20	82	12	64	55	1	0	43	1.10
1718394--1718478	26	3.0	28	75	13	68	36	1	1	61	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1720726--1720766	12	3.6	12	77	12	50	51	7	2	39	1.43
1721145--1721209	16	4.1	17	76	13	59	61	0	0	38	0.96
1721139--1721207	19	3.6	19	80	16	81	60	0	0	39	0.97
1721134--1721234	38	2.6	37	86	10	123	58	0	0	41	0.98
1721142--1721247	15	6.9	16	69	20	50	55	0	0	44	0.99
1721346--1721376	6	5.2	6	92	0	53	16	3	51	29	1.59
1722068--1722130	30	2.0	33	81	9	78	25	4	0	69	1.07
1722081--1722115	18	1.9	18	94	0	61	22	2	0	74	0.95
1722093--1722130	17	2.4	16	86	8	51	21	2	0	76	0.91
1725463--1725530	15	4.1	16	81	14	61	32	1	1	64	1.11

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32